3SZS | pdb_00003szs

Crystal structure analysis of hellethionin D

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NBL	PDB ENTRY 1NBL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	0.1 M sodium iodide, 0.1 M Tris, pH 7.0, 0.2 M magnesium chloride hexahydrate, 1.9 M sodium chloride, protein solution was 45 mg/mL in HEPES diffusion, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
3.18	61.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.829	α = 90
b = 129.829	β = 90
c = 103.994	γ = 90

Symmetry
Space Group	I 4 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2009-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X12	0.9540,1.900	EMBL/DESY, HAMBURG	X12

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1,2,3	1.95	91.8	99.9	0.1224	0.1224	38.36	45.9	32601	32570	-3	-3	22.26

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2,3	1.95	2.05	99.9		0.4054	0.4054	38.36	16.75	4446

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MR SAD	THROUGHOUT	PDB ENTRY 1NBL	1.95	91.8	32601	31827	1622	97.6	0.192	0.19	0.25	0.221	0.28	SHELLS	27.52

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-2.11			-2.11		4.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.758
r_dihedral_angle_4_deg	18.789
r_dihedral_angle_3_deg	10.507
r_dihedral_angle_1_deg	5.237
r_scangle_it	2.026
r_scbond_it	1.301
r_angle_refined_deg	1.131
r_angle_other_deg	0.866
r_mcangle_it	0.756
r_mcbond_it	0.431

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.758
r_dihedral_angle_4_deg	18.789
r_dihedral_angle_3_deg	10.507
r_dihedral_angle_1_deg	5.237
r_scangle_it	2.026
r_scbond_it	1.301
r_angle_refined_deg	1.131
r_angle_other_deg	0.866
r_mcangle_it	0.756
r_mcbond_it	0.431
r_mcbond_other	0.128
r_chiral_restr	0.066
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2322
Nucleic Acid Atoms
Solvent Atoms	378
Heterogen Atoms	52

Software

Software
Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SADABS	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.